Specifications
==============

Sequence source file: "/data/brick1/zmahmoud/africandsi-megassr/megassr-v3/results/hub_GCA_018232005.1/fasta/hub_GCA_018232005.1_genomic.fa"

Definement of microsatellites (unit size / minimum number of repeats):
(1/20) (2/6) (3/5) (4/4) (5/3) (6/3) 

Maximal number of bases interrupting 2 SSRs in a compound microsatellite:  100



RESULTS OF MICROSATELLITE SEARCH
================================

Total number of sequences examined:              30043
Total size of examined sequences (bp):           10151561
Total number of identified SSRs:                 1319
Number of SSR containing sequences:              1143
Number of sequences containing more than 1 SSR:  119
Number of SSRs present in compound formation:    127


Distribution to different repeat type classes
---------------------------------------------

Unit size	Number of SSRs
1	202
2	276
3	142
4	289
5	353
6	57

Frequency of identified SSR motifs
----------------------------------

Repeats	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	32	33	34	35	36	37	38	39	40	41	42	43	44	45	46	47	48	49	50	51	52	53	54	55	56	57	58	59	60	61	62	63	64	65	66	67	68	69	70	71	72	73	74	75	76	77	78	total
A	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	5	4	6	2	1	3	1	3				2	1	1	1	1	1		1					1		2					1					1		1				1																1	1	42
C	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	5	1	6	3	4		3	2		1	1			2	1				1					2		1		1			2		1					1																						38
G	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	8	2	8	6	4	1	3	4	2	1	2	5	4	1	2	2	1	3	3	1			2	1	1		2		1		2	3							1																					76
T	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	5		2	4	1	3	5	2	1	3	1				1		2	1		1			1	2	1			2	1	2		1	1	1				1		1																				46
AC	-	-	-	10	6	2		4	1					1				1	1				1							1																																															28
AG	-	-	-	8	6		2	1													1																																																								18
AT	-	-	-	24	10	6	4	1	2	1			1		1																																																														50
CA	-	-	-	10	6	3	5	2	1		2	2	1				1		1	1	1			1																																																					37
CG	-	-	-			2																																																																							2
CT	-	-	-	4	5	1		2																																																																					12
GA	-	-	-	3	2			1																																																																					6
GT	-	-	-	3	2		3		2	1	1	1		1						1		1	1						1																																																18
TA	-	-	-	16	5	9		1	2				2																																																																35
TC	-	-	-	12	7	4	1			1																																																																			25
TG	-	-	-	10	5	2	5	3	2	2	1	3	1	3	1		2			1	1	1	1				1																																																		45
AAC	-	-			1																																																																								1
AAG	-	-	1	1																																																																									2
AAT	-	-	7	9	2																																																																								18
ACA	-	-	2		1																																																																								3
ACG	-	-	1																																																																										1
AGA	-	-	2																																																																										2
AGC	-	-	1																																																																										1
AGT	-	-	1		1																																																																								2
ATA	-	-	15	1																																																																									16
ATC	-	-	4	1																																																																									5
ATT	-	-	12	2	2		1																																																																						17
CAT	-	-			1																																																																								1
CCA	-	-	1	1																																																																									2
CGC	-	-	1																																																																										1
CTT	-	-	1	1																																																																									2
GAT	-	-		2																																																																									2
GCC	-	-	1																																																																										1
GCG	-	-	1																																																																										1
GGC	-	-	2																																																																										2
GTA	-	-		1																																																																									1
GTC	-	-		1																																																																									1
TAA	-	-	7	1				1																																																																					9
TAC	-	-	1																																																																										1
TAG	-	-	2		1																																																																								3
TAT	-	-	7	2																																																																									9
TCA	-	-	1	3																																																																									4
TCT	-	-	5																																																																										5
TGA	-	-		1		1																																																																							2
TGC	-	-	3																																																																										3
TGT	-	-	2																																																																										2
TTA	-	-	9	5	2	1																																																																							17
TTC	-	-	1	1																																																																									2
TTG	-	-	1	2																																																																									3
AAAC	-	1																																																																											1
AAAG	-	2	1																																																																										3
AAAT	-	17	3	1	1																																																																								22
AAGA	-	2																																																																											2
AATA	-	17	6	3	2				1																																																																				29
AATC	-		1																																																																										1
AATT	-	2																																																																											2
ACAG	-	1																																																																											1
ACAT	-				1																																																																								1
ACCA	-													1																																																															1
ACCT	-	1																																																																											1
ACTC	-	1																																																																											1
AGAC	-			1																		1																																																							2
AGCA	-	1																																																																											1
ATAA	-	10	2	1		1																																																																							14
ATAC	-	1																																																																											1
ATAG	-	2																																																																											2
ATCA	-	1		1																																																																									2
ATGG	-	1																																																																											1
ATGT	-	2	1																																																																										3
ATTG	-	1		1																																																																									2
ATTT	-	11	4	1																																																																									16
CAAA	-	1																																																																											1
CAAT	-							1																																																																					1
CACG	-			1																																																																									1
CAGA	-	1			1																																																																								2
CATC	-		1																																																																										1
CCCT	-	1																																																																											1
CCTA	-	1																																																																											1
CGCA	-				1																																																																								1
CGGT	-	1																																																																											1
CTAC	-			1																																																																									1
CTAG	-		1																																																																										1
CTGC	-	1																																																																											1
CTGT	-	2																																																																											2
CTTT	-	1																																																																											1
GAAA	-	3	1																																																																										4
GAAG	-	1																																																																											1
GAAT	-	1																																																																											1
GAGT	-	1																																																																											1
GATA	-			1																																																																									1
GATG	-	1																																																																											1
GCGG	-	1																																																																											1
GCGT	-	1																																																																											1
GGAC	-				1																																																																								1
GTAT	-										1																																																																		1
GTCT	-	1					1																																																																						2
GTTT	-	1		1																																																																									2
TAAA	-	8	3	2																																																																									13
TACA	-	1	1																																																																										2
TACC	-	1																																																																											1
TACT	-	2																																																																											2
TAGA	-	1																																																																											1
TATC	-	1		1																																																																									2
TATG	-	3								1																																																																			4
TATT	-	15	4	1	2																																																																								22
TCAA	-	1	1																																																																										2
TCTA	-					1																																																																							1
TCTT	-	2	1																																																																										3
TGAA	-		1																																																																										1
TGAG	-	1																																																																											1
TGAT	-							1																																																																					1
TGCA	-	1																																																																											1
TGCC	-		1																																																																										1
TGGA	-	1																																																																											1
TGTA	-	2	2																																																																										4
TGTC	-		1			1																																																																							2
TGTT	-	2																																																																											2
TTAA	-	2																																																																											2
TTAT	-	11		1	1																																																																								13
TTCG	-	1																																																																											1
TTCT	-	1	2	1	1																																																																								5
TTGA	-	3	1																																																																										4
TTGT	-	1																																																																											1
TTTA	-	21	9	2							1																																																																		33
TTTC	-	9	6	4	1																																																																								20
TTTG	-	1																																																																											1
AAAAC	1																																																																												1
AAAAT	4																																																																												4
AAAGA	5																																																																												5
AAAGG		1																																																																											1
AAATA	5	1			1																																																																								7
AAATC	2	1																																																																											3
AAATG	2																																																																												2
AAATT	1																																																																												1
AACCT	3			1	1	1				1																																																																			7
AACTA	1																																																																												1
AAGAA	1																																																																												1
AAGTG	1																																																																												1
AATAA	8	1																																																																											9
AATAC	1		1																																																																										2
AATAG		1																																																																											1
AATCA			1																																																																										1
AATGA	1																																																																												1
AATGG	1																																																																												1
AATTA	2	1																																																																											3
AATTC	1																																																																												1
AATTT	2																																																																												2
ACAAA	1																																																																												1
ACAAC	1																																																																												1
ACAGG	1																																																																												1
ACATG	1																																																																												1
ACCAA	1																																																																												1
ACCTA	1		1	1				1																																																																					4
ACGAA	1																																																																												1
ACGAG	1																																																																												1
ACTTC	1																																																																												1
ACTTG	1																																																																												1
AGGCA	1																																																																												1
AGGTT				1				1																																																																					2
AGTAC	1																																																																												1
AGTCT	1	1																																																																											2
AGTTT		1																																																																											1
ATAAA	6																																																																												6
ATAAG	1																																																																												1
ATACA	2	1																																																																											3
ATACC	1																																																																												1
ATACT	2																																																																												2
ATGAA	2																																																																												2
ATGCC	1																																																																												1
ATGTA	1																																																																												1
ATTAC	1																																																																												1
ATTCC	1	2	2	2		1	1																																																																						9
ATTCG	1																																																																												1
ATTCT	1																																																																												1
ATTGA	1																																																																												1
ATTGT	1																																																																												1
ATTTA	1																																																																												1
ATTTC	1	1	1																																																																										3
ATTTG	2																																																																												2
ATTTT	8																																																																												8
CAAAA	2																																																																												2
CACAA	1																																																																												1
CACGA		1																																																																											1
CACTA	1																																																																												1
CAGTT	1																																																																												1
CATCC	1																																																																												1
CATTC	1	4	1		1																																																																								7
CCCCT	1																																																																												1
CCGCG	1																																																																												1
CCTAA	1		1	1			1	2																																																																					6
CCTCG	1																																																																												1
CGCCG	2																																																																												2
CGCTG	1																																																																												1
CTAAC					1					1																																																																			2
CTAGG		1																																																																											1
CTATG	1																																																																												1
CTATT	1																																																																												1
CTCGA	1																																																																												1
CTCTA	1																																																																												1
CTGAA	1																																																																												1
CTGCC	1																																																																												1
CTGCG	1																																																																												1
CTGTA	1																																																																												1
CTTAG	1																																																																												1
CTTCT	1																																																																												1
CTTTT	4																																																																												4
GAAAT	1																																																																												1
GAATA		1																																																																											1
GAATG	1				1			1																																																																					3
GAGAA	1																																																																												1
GAGTT	1																																																																												1
GATGA		1																																																																											1
GATTA	1																																																																												1
GCGAT	1																																																																												1
GGAAT		2	1	2			1																																																																						6
GGAGG	1																																																																												1
GGCCT	1																																																																												1
GGCGC	1																																																																												1
GGTAT	1																																																																												1
GGTTA		3	2		2		3		1																																																																				11
GTAGT	1																																																																												1
GTGAT	1																																																																												1
GTGTA	1																																																																												1
GTTAG	2				1	2	1								1																																																														7
GTTCC	1																																																																												1
GTTCG	1																																																																												1
GTTGT	1																																																																												1
GTTTA	1																																																																												1
GTTTT	1																																																																												1
TAAAA	7																																																																												7
TAACC				1	1																																																																								2
TAACG	1																																																																												1
TAAGT	1																																																																												1
TAATA	1																																																																												1
TAATT	3																																																																												3
TACAA	2																																																																												2
TACAG	1																																																																												1
TACAT	2																																																																												2
TACTT	1																																																																												1
TAGAA	1																																																																												1
TAGGT	1	1		1		1																																																																							4
TATAT	2																																																																												2
TATTA	3																																																																												3
TATTC	1																																																																												1
TATTG	1																																																																												1
TATTT	4																																																																												4
TCAAA	3																																																																												3
TCATT	1																																																																												1
TCCAT	1																																																																												1
TCGAC	1																																																																												1
TCTCC	1																																																																												1
TCTCG	3																																																																												3
TCTCT	1																																																																												1
TCTGT	1																																																																												1
TCTTA	1																																																																												1
TCTTC	2																																																																												2
TCTTT	1																																																																												1
TGAAA	3																																																																												3
TGAAC	1																																																																												1
TGAAT		1																																																																											1
TGAGC				1																																																																									1
TGAGT	1																																																																												1
TGATT	3	1																																																																											4
TGCAA	1																																																																												1
TGCCA	1																																																																												1
TGGAA		1			1																																																																								2
TGGCA		1																																																																											1
TGTAA	1																																																																												1
TGTAT	1																																																																												1
TGTGT	2																																																																												2
TTAAA	3																																																																												3
TTAAT	3																																																																												3
TTAGG	4			1																																																																									5
TTAGT	2																																																																												2
TTATA	1																																																																												1
TTATC	1																																																																												1
TTATT	3																																																																												3
TTCAA	1		1																																																																										2
TTCAT	1																																																																												1
TTCCA		1	1	1																																																																									3
TTCCT	1																																																																												1
TTCTA	1		2																																																																										3
TTCTT	1																																																																												1
TTGAA	2																																																																												2
TTGAG	1																																																																												1
TTGTA	2																																																																												2
TTGTG	1																																																																												1
TTTAA	3																																																																												3
TTTAT	8																																																																												8
TTTCA	2	1																																																																											3
TTTCC	1																																																																												1
TTTCG	1																																																																												1
TTTCT	2																																																																												2
TTTGA	1																																																																												1
TTTGG	1																																																																												1
TTTTA	10	1	1																																																																										12
TTTTC	2																																																																												2
TTTTG	1					1																																																																							2
AAAACA	1																																																																												1
AAAATC	1																																																																												1
AAAGAC	1																																																																												1
AAAGCT		1																																																																											1
AAATAA	2																																																																												2
AAGACA	1																																																																												1
ACAAAT		1																																																																											1
AGATAA	1																																																																												1
AGGCGG				1																																																																									1
AGTAAT	1																																																																												1
ATTAAC	1																																																																												1
ATTAAT	1																																																																												1
ATTCTG		1																																																																											1
ATTTCA	1																																																																												1
ATTTCT	1																																																																												1
ATTTTG	1																																																																												1
ATTTTT	1																																																																												1
CAAGAC	1	1																																																																											2
CATTTA	1																																																																												1
CCGGGA	1																																																																												1
CGAAAC	1																																																																												1
CGATCC				1																																																																									1
CGCCCA	1																																																																												1
CGTAAC						1																																																																							1
CTGATT	1																																																																												1
GAATAT	1																																																																												1
GACAGT		1																																																																											1
GACATA	1																																																																												1
GATTTT	2																																																																												2
GGGGGC	1																																																																												1
GTATTG	2																																																																												2
TAAAAA	1																																																																												1
TAAATA	1																																																																												1
TAAATT	1																																																																												1
TATGTA	2																																																																												2
TATTTT	1																																																																												1
TCAAAA	2																																																																												2
TCTGTC		1																																																																											1
TGAAAA	1																																																																												1
TGATTC	1																																																																												1
TGTCAC	1																																																																												1
TTAACA	1																																																																												1
TTACAA	1																																																																												1
TTATTT	1																																																																												1
TTTAAT	1																																																																												1
TTTCTT	1																																																																												1
TTTGAC	1																																																																												1
TTTTTA	2																																																																												2
TTTTTC	2																																																																												2

Frequency of classified repeat types (considering sequence complementary)
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Repeats	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	32	33	34	35	36	37	38	39	40	41	42	43	44	45	46	47	48	49	50	51	52	53	54	55	56	57	58	59	60	61	62	63	64	65	66	67	68	69	70	71	72	73	74	75	76	77	78	total
A/T	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	10	4	8	6	2	6	6	5	1	3	1	2	1	1	2	1	3	1	1	1			1	3	1	2		2	1	2	1	1	1	1		1		2		1		1																1	1	88
C/G	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	13	3	14	9	8	1	6	6	2	2	3	5	4	3	3	2	1	3	4	1			2	3	1	1	2	1	1		4	3	1					1	1																					114
AC/GT	-	-	-	33	19	7	13	9	6	3	4	6	2	5	1		3	1	2	3	2	2	3	1			1		1	1																																															128
AG/CT	-	-	-	27	20	5	3	4		1											1																																																								61
AT/AT	-	-	-	40	15	15	4	2	4	1			3		1																																																														85
CG/CG	-	-	-			2																																																																							2
AAC/GTT	-	-	5	2	2																																																																								9
AAG/CTT	-	-	10	3																																																																									13
AAT/ATT	-	-	57	20	6	1	1	1																																																																					86
ACC/GGT	-	-	1	1																																																																									2
ACG/CGT	-	-	1	1																																																																									2
ACT/AGT	-	-	4	1	2																																																																								7
AGC/CTG	-	-	4																																																																										4
ATC/ATG	-	-	5	7	1	1																																																																							14
CCG/CGG	-	-	5																																																																										5
AAAC/GTTT	-	7		1																																																																									8
AAAG/CTTT	-	20	11	5	2																																																																								38
AAAT/ATTT	-	110	31	12	6	1			1		1																																																																		162
AACC/GGTT	-													1																																																															1
AACG/CGTT	-	1																																																																											1
AAGC/CTTG	-	1																																																																											1
AAGG/CCTT	-	1																																																																											1
AAGT/ACTT	-	2																																																																											2
AATC/ATTG	-	6	3	2				2																																																																					13
AATG/ATTC	-	1	1																																																																										2
AATT/AATT	-	4																																																																											4
ACAG/CTGT	-	5	1	1	1	1	1															1																																																							11
ACAT/ATGT	-	9	4		1					1	1																																																																		16
ACCG/CGGT	-	1																																																																											1
ACCT/AGGT	-	3		1																																																																									4
ACGC/CGTG	-	1		1	1																																																																								3
ACGG/CCGT	-				1																																																																								1
ACTC/AGTG	-	3																																																																											3
AGAT/ATCT	-	4		2		1																																																																							7
AGCT/AGCT	-		1																																																																										1
AGGC/CCTG	-	1	1																																																																										2
AGGG/CCCT	-	1																																																																											1
ATCC/ATGG	-	3	1																																																																										4
ATGC/ATGC	-	1																																																																											1
CCCG/CGGG	-	1																																																																											1
AAAAC/GTTTT	6					1																																																																							7
AAAAG/CTTTT	16																																																																												16
AAAAT/ATTTT	63	3	1		1																																																																								68
AAACC/GGTTT	2																																																																												2
AAACG/CGTTT	2																																																																												2
AAACT/AGTTT	4	1																																																																											5
AAAGG/CCTTT	2	1																																																																											3
AAAGT/ACTTT	1																																																																												1
AAATC/ATTTG	11	2	1																																																																										14
AAATG/ATTTC	14	2	1																																																																										17
AAATT/AATTT	18	1																																																																											19
AACAC/GTGTT	6																																																																												6
AACAG/CTGTT	1																																																																												1
AACCG/CGGTT	1																																																																												1
AACCT/AGGTT	12	4	4	7	6	4	5	4	1	2					1																																																														50
AACGG/CCGTT	1																																																																												1
AACGT/ACGTT	1																																																																												1
AACTC/AGTTG	3																																																																												3
AACTG/AGTTC	3																																																																												3
AACTT/AAGTT	1																																																																												1
AAGAG/CTCTT	5																																																																												5
AAGAT/ATCTT	3																																																																												3
AAGCT/AGCTT	1																																																																												1
AAGGC/CCTTG	1																																																																												1
AAGTC/ACTTG	1																																																																												1
AAGTG/ACTTC	2																																																																												2
AATAC/ATTGT	10	1	1																																																																										12
AATAG/ATTCT	5	2	2																																																																										9
AATAT/ATATT	7																																																																												7
AATCG/ATTCG	1																																																																												1
AATCT/AGATT	1																																																																												1
AATGC/ATTGC	1																																																																												1
AATGG/ATTCC	5	10	5	5	3	1	2	1																																																																					32
AATGT/ACATT	5																																																																												5
AATTC/AATTG	5	1	1																																																																										7
ACACG/CGTGT		1																																																																											1
ACACT/AGTGT	3																																																																												3
ACAGG/CCTGT	1																																																																												1
ACAGT/ACTGT	3																																																																												3
ACATC/ATGTG	1																																																																												1
ACATG/ATGTC	1																																																																												1
ACCAT/ATGGT	2																																																																												2
ACGAG/CGTCT	4																																																																												4
ACTAG/AGTCT	1	1																																																																											2
ACTAT/AGTAT	2																																																																												2
ACTCG/AGTCG	2																																																																												2
ACTCT/AGAGT	1																																																																												1
AGAGG/CCTCT	1																																																																												1
AGATG/ATCTC		1																																																																											1
AGCAT/ATGCT	1																																																																												1
AGCCT/AGGCT		1																																																																											1
AGCGC/CGCTG	2																																																																												2
AGCTC/AGCTG				1																																																																									1
AGGCC/CCTGG	1																																																																												1
AGGCG/CCTCG	1																																																																												1
AGGGC/CCCTG	1																																																																												1
AGGGG/CCCCT	2																																																																												2
ATCCC/ATGGG	1																																																																												1
ATCGC/ATGCG	1																																																																												1
ATGCC/ATGGC	2	1																																																																											3
CCGCG/CGCGG	4																																																																												4
AAAAAC/GTTTTT	1																																																																												1
AAAAAG/CTTTTT	3																																																																												3
AAAAAT/ATTTTT	8																																																																												8
AAAATC/ATTTTG	6																																																																												6
AAAATG/ATTTTC	1																																																																												1
AAAATT/AATTTT	1																																																																												1
AAACCG/CGGTTT	1																																																																												1
AAAGAC/CTTTGT	2																																																																												2
AAAGAT/ATCTTT	1																																																																												1
AAAGCT/AGCTTT		1																																																																											1
AAAGTC/ACTTTG	1																																																																												1
AAATAC/ATTTGT		1																																																																											1
AAATAG/ATTTCT	1																																																																												1
AAATAT/ATATTT	1																																																																												1
AAATGT/ACATTT	1																																																																												1
AAATTG/AATTTC	1																																																																												1
AAATTT/AAATTT	1																																																																												1
AACATT/AATGTT	2																																																																												2
AACCGT/ACGGTT						1																																																																							1
AAGACC/CTTGGT	1	1																																																																											2
AATACC/ATTGGT	2																																																																												2
AATAGT/ACTATT	1																																																																												1
AATATG/ATATTC	1																																																																												1
AATATT/AATATT	1																																																																												1
AATCAG/ATTCTG	2	1																																																																											3
AATTAC/AATTGT	1																																																																												1
ACAGAG/CTCTGT		1																																																																											1
ACAGTG/ACTGTC	1	1																																																																											2
ACATAG/ATGTCT	1																																																																												1
ACATAT/ATATGT	2																																																																												2
ACCGGG/CCCGGT	1																																																																												1
ACGCCC/CGTGGG	1																																																																												1
AGGCGG/CCGCCT				1																																																																									1
ATCCCG/ATCGGG				1																																																																									1
CCCCCG/CGGGGG	1																																																																												1
